Browser Interface unresponsive after few clicks

stefan.bohn · November 8, 2022, 12:45pm

Hello,

I am running Cryosparc live on a local server. While it was possible before to set up jobs and complete them correctly, the live session view is unresponsive after two or three clicks and requires a reload(hence no threshold adjustments possible, etc.). cryosparcm restart did not resolve the issue.

Following the trouble-shooting guide (Troubleshooting - CryoSPARC Guide) I recorded the network_chrome.har and console_chrome.log but do not know how to proceed from here - post the content of those files here? Or send those as attachments?

Best,
Stefan.

wtempel · November 8, 2022, 3:50pm

Welcome to the forum @stefan.bohn and thank you for recording the information.
If the files are not too big and they do not contain confidential information, you may post the files’ contents here.

stefan.bohn · November 8, 2022, 4:34pm

Hey there,

thanks for getting back. I think the size is fine for console log only. Please see below.

console log:

index.72d41794.js:1 Exposure Stage: classification 1290 ready
index.72d41794.js:1 Exposure [conditionalLoad] micrograph image 1290 ready
index.72d41794.js:1 command-vis getMicrographImage
index.72d41794.js:1 command:vis get_individual_data_mic {project_uid: 'P2', session_uid: 'S1', exposure_uid: 1290, lp_filter_A: null} true
index.72d41794.js:1 data subscribe: liveRollingExposures rollingExposures args: (3) ['P2', 'S1', 1290]
index.72d41794.js:1 data subscribe: liveSingleExposure singleExposure args: (3) ['P2', 'S1', 1290]
index.72d41794.js:1 data subscribe: liveClass2DJob singleJob args: (2) ['P2', 'J4']
index.72d41794.js:1 INFO virtual list mounted
index.72d41794.js:1 INFO Scale and center 1024 1024 610 648
index.72d41794.js:1 command:vis get_individual_data_mic 620.40 ms
index.72d41794.js:1 Exposure Micrograph 1290 1401.700 ms
index.72d41794.js:1 Exposure [conditionalLoad] micrograph picks 1290 ready
index.72d41794.js:1 command-rtp getManualPicks
index.72d41794.js:1 command:rtp get_individual_data_picks {project_uid: 'P2', session_uid: 'S1', exposure_uid: 1290, picker_type: 'manual'}
index.72d41794.js:1 command-rtp getBlobPicks
index.72d41794.js:1 command:rtp get_individual_data_picks {project_uid: 'P2', session_uid: 'S1', exposure_uid: 1290, picker_type: 'blob'}
index.72d41794.js:1 command-rtp getTemplatePicks
index.72d41794.js:1 command:rtp get_individual_data_picks {project_uid: 'P2', session_uid: 'S1', exposure_uid: 1290, picker_type: 'template'}
index.72d41794.js:1 command:rtp get_individual_data_picks 112.10 ms
index.72d41794.js:1 command:rtp get_individual_data_picks 205.60 ms
index.72d41794.js:1 command:rtp get_individual_data_picks 204.20 ms
index.72d41794.js:1 INFO All exposure data loaded in 2635.00 ms.
index.72d41794.js:1 data subscribe-ready: liveRollingExposures rollingExposures args: (3) ['P2', 'S1', 1290]
index.72d41794.js:1 data subscribe-ready: liveSingleExposure singleExposure args: (3) ['P2', 'S1', 1290]
index.72d41794.js:1 data subscribe-ready: liveClass2DJob singleJob args: (2) ['P2', 'J4']
index.72d41794.js:1 Exposure Tab: overview 1290 ready
index.72d41794.js:1 Exposure [conditionalLoad] micrograph picks 1290 ready
index.72d41794.js:1 command-rtp getManualPicks
index.72d41794.js:1 command:rtp get_individual_data_picks {project_uid: 'P2', session_uid: 'S1', exposure_uid: 1290, picker_type: 'manual'}
index.72d41794.js:1 command-rtp getBlobPicks
index.72d41794.js:1 command:rtp get_individual_data_picks {project_uid: 'P2', session_uid: 'S1', exposure_uid: 1290, picker_type: 'blob'}
index.72d41794.js:1 command-rtp getTemplatePicks
index.72d41794.js:1 command:rtp get_individual_data_picks {project_uid: 'P2', session_uid: 'S1', exposure_uid: 1290, picker_type: 'template'}
index.72d41794.js:1 command:rtp get_individual_data_picks 107.70 ms
index.72d41794.js:1 command:rtp get_individual_data_picks 167.00 ms
index.72d41794.js:1 command:rtp get_individual_data_picks 161.70 ms
index.72d41794.js:1 INFO threshold values -> updating ice_thickness_rel 
 Min val: NaN -> NaN (NaN)
 Max val: NaN -> NaN (NaN)
 Local min: NaN Local max: NaN
 Range min: NaN Range max: NaN

index.72d41794.js:1 INFO Threshold control mounted found_at {minValue: 1667817991405, maxValue: 1667840299862, padding: 2230846.7, rangeMin: 1667815760558.3, rangeMax: 1667842530708.7, …}
index.72d41794.js:1 INFO Attribute plot mount found_at
index.72d41794.js:1 INFO Threshold control mounted average_defocus {minValue: 1000, maxValue: 38863.73134151312, padding: 3787.4, rangeMin: -2787.4, rangeMax: 42651.4, …}
index.72d41794.js:1 INFO Attribute plot mount average_defocus
index.72d41794.js:1 INFO Threshold control mounted ctf_fit_to_A {minValue: 0.9508804329243714, maxValue: 51.299999356269836, padding: 5.035900000000001, rangeMin: -4.08, rangeMax: 56.34, …}
index.72d41794.js:1 INFO Attribute plot mount ctf_fit_to_A
index.72d41794.js:1 INFO Threshold control mounted ice_thickness_rel {minValue: NaN, maxValue: NaN, padding: NaN, rangeMin: NaN, rangeMax: NaN, …}
wNumb.818538ef.js:1 Uncaught (in promise) Error: noUiSlider: 'range' value isn't numeric.
    at t.handleEntryPoint (wNumb.818538ef.js:1:5331)
    at new t (wNumb.818538ef.js:1:3342)
    at Object.ut [as t] (wNumb.818538ef.js:1:7538)
    at wNumb.818538ef.js:1:12795
    at Array.forEach (<anonymous>)
    at Be (wNumb.818538ef.js:1:12673)
    at Object.Ie [as create] (wNumb.818538ef.js:1:27282)
    at Overview.4d34f45b.js:9:9040
    at cn (vendor.5a86cc54.js:1:176)
    at Array.map (<anonymous>)
t.handleEntryPoint @ wNumb.818538ef.js:1
t @ wNumb.818538ef.js:1
ut @ wNumb.818538ef.js:1
(anonymous) @ wNumb.818538ef.js:1
Be @ wNumb.818538ef.js:1
Ie @ wNumb.818538ef.js:1
(anonymous) @ Overview.4d34f45b.js:9
cn @ vendor.5a86cc54.js:1
(anonymous) @ vendor.5a86cc54.js:4
Pt @ vendor.5a86cc54.js:4
Promise.then (async)
Tn @ vendor.5a86cc54.js:4
Vr @ vendor.5a86cc54.js:4
(anonymous) @ vendor.5a86cc54.js:4
N @ index.72d41794.js:3
await in N (async)
(anonymous) @ index.72d41794.js:3
cn @ vendor.5a86cc54.js:1
(anonymous) @ vendor.5a86cc54.js:4
Pt @ vendor.5a86cc54.js:4
Promise.then (async)
Tn @ vendor.5a86cc54.js:4
Vr @ vendor.5a86cc54.js:4
(anonymous) @ vendor.5a86cc54.js:4
(anonymous) @ SingleSession.fd48a0b6.js:1
i @ vendor.5a86cc54.js:4
set @ index.72d41794.js:1
Nd @ index.72d41794.js:3
(anonymous) @ Navigation.344b5e7d.js:1
y @ Navigation.344b5e7d.js:1
index.72d41794.js:1 INFO updateAttributeThreshold ice_thickness_rel NaN NaN
index.72d41794.js:1 command-rtp updateAttributeThreshold
index.72d41794.js:1 command:rtp update_threshold {project_uid: 'P2', session_uid: 'S1', attribute: 'ice_thickness_rel', min_val: NaN, max_val: NaN}
index.72d41794.js:1 command:rtp update_threshold 82.10 ms
index.72d41794.js:1 INFO callMethod: allFilteredExposuresTable (2) ['P2', 'S1']
index.72d41794.js:1 INFO All exposure data loaded in 2164.50 ms.

stefan.bohn · November 8, 2022, 4:35pm

And the network.har file is too big to post here.

wtempel · November 9, 2022, 5:49pm

Please can you enter an icli shell:
cryosparcm icli
and post the output of
rtp.get_exposure('P2', 'S1', '1290', 'groups.exposure.ctf_stats')

stefan.bohn · November 10, 2022, 11:19am

Hello,

no output was generated:

cryosparcm icli
Python 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:53)
Type ‘copyright’, ‘credits’ or ‘license’ for more information
IPython 7.33.0 – An enhanced Interactive Python. Type ‘?’ for help.

connecting to su-rz085338-1.scidom.de:38002 …
cli, rtp, db, gfs and tools ready to use

In [1]: rtp
Out[1]: <cryosparc_compute.client.CommandClient at 0x7f8aa3888a50>

In [2]: rtp.get_exposure(‘P2’, ‘S1’, ‘1290’, ‘groups.exposure.ctf_stats’)

In [3]:

wtempel · November 10, 2022, 4:00pm

… likely my fault because I provided the incorrect command. I apologize. The third parameter should be numeric:
rtp.get_exposure('P2', 'S1', 1290, 'groups.exposure.ctf_stats')
Please can you try again?

stefan.bohn · November 11, 2022, 6:37am

This also seems to not be liked:

In [1]: rtp.get_exposure('P2', 'S1', 1290, 'groups.exposure.ctf_stats')
   ...:
Out[1]:
{'groups': {'exposure': {'ctf_stats': {'cross_corr': [0.0],
    'ctf_fit_to_A': [20.117647171020508],
    'df_range': [[1000.620849609375, 1272.7379150390625]],
    'df_tilt_normal': [[-0.006880586035549641, 0.038908228278160095]],
    'diag_image_path': ['S1/ctfestimated/FoilHole_2997733_Data_2993577_2993579_20221103_193246_EER_patch_aligned_ctf_diag_2D.mrc'],
    'fit_data_path': ['S1/ctfestimated/FoilHole_2997733_Data_2993577_2993579_20221103_193246_EER_patch_aligned_ctf_diag_plt.npy'],
    'ice_thickness_rel': [1.0070626735687256],
    'spectrum_dim': [2160],
    'type': ['spline']}}}}

wtempel · November 11, 2022, 7:48pm

rtp.get_exposure() may seem a little unfriendly at first , but in this case worked as expected.
I will request additional information in a direct message.

wtempel · November 21, 2022, 4:50pm

We are still looking into this issue.
Please can you (tested in Chrome browser, may work in other browsers)

Navigate to the Overview tab on the left hand side of the relevant CryoSPARC Live session’s browser window.
Open the browser console (More tools|Developer tools)

In the console, type:

window.localStorage.setItem('cryosparc_debug', true);
copy(_live.allExposuresAttributes.filter(e => isNaN(e.ice_thickness_rel)))

Paste the clipboard content into a text file and e-mail us the text file.

Thanks.